I have successfully done my MD simulation and now i am calculating binding energy but i don't know how to calculate this?
Plz guide me. I shall be very thankful to you.
please give a little bit more more deatail about the software you used for MD simulation.
If you have used GROMACS for MD simulations-
For the extraction of the snapshots from the MD trajectory for binding free energy calculation, you can use the command
gmx trjconv -s .tpr -f .xtc -o .xtc -n index.ndx -pbc mol -ur compact -b -e -dt
Anu Manhas respected mam, thanks for the reply. Mam i just apply command and now they are asking me "select group for out put"
Group 0 ( System) has 69424 elements
Group 1 ( Protein) has 8134 elements
Group 2 ( Protein-H) has 4024 elements
Group 3 ( C-alpha) has 510 elements
Group 4 ( Backbone) has 1530 elements
Group 5 ( MainChain) has 2038 elements
Group 6 ( MainChain+Cb) has 2516 elements
Group 7 ( MainChain+H) has 2524 elements
Group 8 ( SideChain) has 5610 elements
Group 9 ( SideChain-H) has 1986 elements
Group 10 ( Prot-Masses) has 8134 elements
Group 11 ( non-Protein) has 61290 elements
Group 12 ( Other) has 118 elements
Group 13 ( LIG) has 118 elements
Group 14 ( NA) has 56 elements
Group 15 ( CL) has 42 elements
Group 16 ( Water) has 61074 elements
Group 17 ( SOL) has 61074 elements
Group 18 ( non-Water) has 8350 elements
Group 19 ( Ion) has 98 elements
Group 20 ( LIG) has 118 elements
Group 21 ( NA) has 56 elements
Group 22 ( CL) has 42 elements
Group 23 ( Water_and_ions) has 61172 elements
Group 24 ( Protein_LIG) has 8252 elements
which group should i select?
Anu Manhas respected tell, also give me some information about putting starting frame, final frame and time interval
i have total 1002 frames(10ns simulation) and i want to extract 100 snapshot at every 50 ps of stable interval from 5 to 10 ns. Now what i have to do?
plz reply.
Shafi Ullah Khan Martin Klvana respected sir, thanks for the reply. I am using gromacs for md simulation.
Is it possible to obtain accurate binding free energies with high confidence from an ensemble of 100 configurations? No. What to do? Collect the ligand-protein energies every 10-20 fs, not every 50 ps.
Is it possible to obtain accurate binding free energies with high confidence by disregarding the solvation of the ligand by water molecules, sodium ions, and chloride ions? No. From the ligand's perspective, the protein is simply a part of the solvent . . .
Martin Klvana respected sir, i am just doing training. This is not my actual simulation. I am just making sure that i can perform simulation.After this i will come towards my actual simulation.
Thanks
As you have saved trajectory at the interval of 10ns, thus, you might have obtained 1001 frames. Now you want to extract last 100 snapshot obtained at every 50ps, in that case, you can chose 500 frame as your b value and 1001 as your e value and 50 for dt.
B is for first frame (ps) and e is for the last frame (ps) to read from trajectory
Command
gmx trjconv -s md_0_50.tpr -f md_0_50_noPBC.xtc -o md_0_50_noPBC30-50ns.xtc -n index.ndx -pbc mol -ur compact -b 500 -e 1001 -dt 50
Anu Manhas Thanks a lot ma'am. I did it and i got 11 frames. Respected ma'am i just want to ask you that what is the difference between frame and snapshot?
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